Supplemental Methods - Epigenenomics of Sample_Group in Heart Failure
Mark E. Pepin
17 January, 2022
Code Author: Mark E. Pepin, MD, PhD, MS Contact: pepinme@gmail.com Institution: Heidelberg University Hospital Location: 669 Neuenheimer Feld, Institute for Experimental Cardiology, 69120 Heidelberg, Germany
Preliminary Setup
Parameters
Define the parameters used, along with the conditions required for the current analysis. This segment must be modified for each analysis performed.
##Set the experimental conditions [MUST DO THIS MANUALLY]
Run_tS<-Sys.time()
TREATMENT=c("CON", "DCM")
CELL=c("heart")
STATISTIC = 0.01 #P statistic threshold used in this combination.
VARIABLE = TREATMENT
COMPARISON= paste0(CELL[1], "_",VARIABLE[2], "_vs_", VARIABLE[1])
# Candidate Gene Selection (RNA-sequencing) EDIT THIS LIST BASED ON INTERESTS.
GENES=c("LEP", "ADIPOQ", "PLIN1")
VAR1="Treatment"
VAR2="Diabetes"
# Single Bar Graph
library(dplyr)
my_comparisons <- list( c("CON", "DCM")) # Comparisons to make
## Create color based on Genotype
ann_colors = list(Treatment = c(DCM="darkgray", CON = "darkcyan"))
TreatmentColors<-ann_colors$Treatment
ann_colorTable<-as.data.frame(ann_colors)
ann_colGroup<-subset(ann_colorTable, rownames(ann_colorTable) %in% TREATMENT)
ann_colListGroup<-list(ann_colors$Treatment)
ann_colGroupVec<-ann_colGroup$Treatment
names(ann_colGroupVec)<-as.factor(rownames(ann_colGroup))
GROUP_colors<-list(ann_colGroupVec=ann_colGroupVec)
# Create Output Folder Structure
ifelse(!dir.exists(file.path(paste0("../2_Output/"))), dir.create(file.path(paste0("../2_Output/"))), FALSE)## [1] FALSEifelse(!dir.exists(file.path(paste0("../2_Output/", COMPARISON))), dir.create(file.path(paste0("../2_Output/", COMPARISON))), FALSE)## [1] FALSEPackages
if (!require("pacman")) install.packages("pacman")
pacman::p_load(dplyr, Hmisc, openxlsx, corrplot, RColorBrewer, kableExtra, ggplot2, gridExtra, ggpubr, ggsignif, DESeq2, data.table, GenomicFeatures, biomaRt, Haplin, pheatmap, calibrate, ggrepel, tidyr, gtools)Genome-wide DNA methylation - Illumina(R) HumanMethylation 450k Methylation
library(minfi)
library(limma)
library(shinyMethyl)
library(dplyr)
library(IlluminaHumanMethylation450kmanifest)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(RColorBrewer)
#########Part 1: Importing the Data
#Parameters
##Get the array annotation
annoM450k<-getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
annoM450k<-dplyr::select(as.data.frame(annoM450k), Name, chr, pos, Relation_to_Island, UCSC_RefGene_Name, UCSC_RefGene_Accession, UCSC_RefGene_Group, Regulatory_Feature_Group)
#Import the sample sheet
targets<-read.metharray.sheet(base="../1_Input/IDAT", pattern=".csv")## [1] "../1_Input/IDAT/SampleSheet.csv" #Import the annotation file
AnnoTargets<-targets
targets$ID <- paste(targets$Sample_Group,targets$Sample_Name,sep=".")
targets$Sample_Well<-AnnoTargets$Sample_Well
targets$Sample_Plate<-AnnoTargets$Sample_Plate
targets$Sample_Group<-AnnoTargets$Sample_Group
targets$Sample_Group<-factor(targets$Sample_Group, levels = c("CON", "DCM"))
targets$Sex<-AnnoTargets$Sex
targets$Outcome<-AnnoTargets$Outcome
targets$Conc<-AnnoTargets$Conc
targets$Col_ID<-AnnoTargets$Col_ID
targets$Tissue<-AnnoTargets$Tissue
targets<-targets %>% filter(Tissue %in% CELL)
#Import the array data from input directory (red and green .idat files)
RGSet<-read.metharray.exp(base = "../1_Input/IDAT", targets = targets, verbose = TRUE)
sampleNames(RGSet)<-targets$Sample_Name
##Quality Control
#First step is to identify CpGs that failed to identify methylated positions (defined by expression intensity that reflects background levels)
detP<-detectionP(RGSet)
PLOT.COL <- brewer.pal(8,"Dark2")
##Detection P-value Plot
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_detectionP.pdf"))
par(mfrow=c(1,1))
barplot(colMeans(detP), col=PLOT.COL[factor(targets$Sample_Group)],
cex.names=0.8, ylim=c(0,0.005), ylab="Mean detection p-values")
abline(h=0.05,col="red")
legend("topleft", legend=levels(factor(targets$Sample_Group)), fill=PLOT.COL,
bg="white")
dev.off()## quartz_off_screen
## 2## Filter RGSet by detection P-value
keep <- colMeans(detP) < 0.05
RGSet <- RGSet[,keep]
RGSet## class: RGChannelSet
## dim: 622399 10
## metadata(0):
## assays(2): Green Red
## rownames(622399): 10600313 10600322 ... 74810490 74810492
## rowData names(0):
## colnames(10): A1_biopsy_bo A2_biopsy_bo ... NF2LV NF3LV
## colData names(17): Sample_Name Sample_Well ... ID filenames
## Annotation
## array: IlluminaHumanMethylation450k
## annotation: ilmn12.hg19##QC Report
qcReport(RGSet, sampNames=targets$ID, sampGroups=targets$Sample_Group, pdf="qcReport.pdf")## quartz_off_screen
## 2#
par(mfrow=c(1,1))
barplot(colMeans(detP), col=PLOT.COL[factor(targets$Sample_Group)], las=2,
cex.names=0.8, ylim=c(0,0.005), ylab="Mean detection p-values")
abline(h=0.05,col="red")
legend("topleft", legend=levels(factor(targets$Sample_Group)), fill=PLOT.COL,
bg="white")
# #Determine the fraction of "failed" CpG probes (those which failed to identify a methylated CpG)
# colMeans(failed)
#Convert R/G to Methylated/Unmethylated in an object of class MethylSet
MSet<-preprocessRaw(RGSet)
#QC data
qc<-getQC(MSet)
plotQC(qc)
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_QC.Methyl.pdf"))
plotQC(qc)
dev.off()## quartz_off_screen
## 2##Density plot
# densityPlot(RGSet, sampGroups = targets$Sample_Group, main= "Beta", xlab = "Beta")
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_densityPlot.pdf"))
densityPlot(RGSet, sampGroups = targets$Sample_Group, main= "Beta", xlab = "Beta")
dev.off()## quartz_off_screen
## 2densityBeanPlot(RGSet, sampGroups = targets$Sample_Group)
pdf(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_BeanPlot.pdf"))
densityBeanPlot(RGSet, sampGroups = targets$Sample_Group)
dev.off()## quartz_off_screen
## 2qcReport(RGSet, pdf= paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_qcReport.pdf"))## quartz_off_screen
## 2# #Convert to a shinyMethyl dataset (nice summary of the quality control)
# summarized.data <- shinySummarize(RGSet)
# runShinyMethyl(summarized.data)
gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE)
beta.all<-getBeta(RGSet)
write.csv(beta.all, "../1_Input/EPIC.betaValues.csv")Supplementary Figure S1: Outlier Analysis and Detection P-Value
par(mfrow=c(1,1))
barplot(colMeans(detP), col=PLOT.COL[factor(targets$Sample_Group)], las=2,
cex.names=0.8, ylim=c(0,0.005), ylab="Mean detection p-values")
abline(h=0.05,col="red")
legend("topleft", legend=levels(factor(targets$Sample_Group)), fill=PLOT.COL,
bg="white")Supplemental Figure 1
Figure S2: SNPs in Methylation Data
SNPs have been shown to confound the interpretation of methylation arrays when mutations exist within the CpG sites. To address this concern, a package called “MethylToSNP” exists to identify novel SNPs based on methylation array data, which has been proposed to reduce the number of CpGs that are filtered. Using this approach, CpGs were identified as putative SNPs which are likely influenced by minor allele fractions (MAFs). Although putative SNP identification is not warranted from the single-source iPSCs, SNP identification was performed on the cardiac biopsy-derived differential methylation data.
{r SNPs, fig.cap = "Supplemental Figure S4: Putative SNP Identification from CpG Probe Intensity"} # #Remove SNPs # ##Option 1: Built-in function that removes all known SNPs # gRatioSet_noSNPs<-dropLociWithSnps(gRatioSet.quantile, snps = c("SBE", "CpG"), maf = 0) # ##Option 2: Identify putative SNPs using methylation barcoding (i.e. "gap hunting") # library("MethylToSNP") # library("RColorBrewer") # library("pheatmap") # library("magrittr") # Mvalues<-as.data.frame(getM(MSet)) # x <- MethylToSNP(MSet,verbose=TRUE) # x$CpG_ID<-rownames(x) # ### # pdf(file="../2_Output/Putative.SNPs.pdf", width = 10, height = 5) #Print Putative SNP Methylation # plotPotentialSNPs(x, MSet) # dev.off() # plotPotentialSNPs(x, MSet) # SNPs<-merge(x, as.data.frame(getM(MSet)), by = "row.names") # write.csv(SNPs, "../2_Output/SNPs.csv") # SNPs_matrix<-SNPs %>% set_rownames(.$Row.names) # SNPs_matrix<-SNPs_matrix[,7:ncol(SNPs_matrix)] %>% as.matrix() # SNPs_matrix<-SNPs_matrix[!is.infinite(rowSums(SNPs_matrix)),] #One infinite value exists!! (took ~2-3 days to troubleshoot) # # Index # targets<-read.metharray.sheet(base="../1_Input/IDAT", pattern=".csv") # rownames(targets)<-targets$Sample_Name # Index_SNPs<-targets[colnames(SNPs_matrix),] %>% dplyr::select(Sample_Group) # ann_colors = list(Sample_Group = c(DCM="#1b9e77", CON = "#d95f02")) # paletteLength <- 100 # myColor <- colorRampPalette(c("dodgerblue4", "white", "gold2"))(paletteLength) # ann_colors = list(Sample_Group = c(DCM="#1b9e77", # CON = "#d95f02")) # # heatmap_SNP<-pheatmap::pheatmap(SNPs_matrix, scale="row", #Heatmap of SNPs # cluster_cols = TRUE, # cluster_rows = TRUE, # angle_col = 45, # fontsize_col = 8, # color = myColor, # show_rownames = FALSE, # border_color = NA, # annotation_colors = ann_colors, # annotation_col = Index_SNPs, # filename = paste0("../2_Output/SNPS.heatmap.pdf")) # pheatmap(SNPs_matrix, scale="row", #Heatmap of SNPs # cluster_cols = TRUE, # cluster_rows = TRUE, # cutree_cols = 3, # cutree_rows = 4, # fontsize_col = 8, # color = myColor, # show_rownames = FALSE, # border_color = NA, # annotation_colors = ann_colors, # annotation_col = Index_SNPs) #
Figure 2/3A: MDS Plot - Unsupervised Clustering by “Sample_Group”
Because such a robust racial signature in cardiac DNA methylation was seen in the pilot analysis, we reproduced the unsupervised method in the larger cohort. This time, we continue to see a distinct racial difference. Furthermore, we found that this racially-determined clustering persisted to among the 500,000 most-variable CpG probes in the EPIC array.
PCA
#Plot Features of the PCA
library(dplyr)
library(plotly)
##Import the data to be used for PCA
Index_PCA<-targets
rownames(Index_PCA)<-Index_PCA$Sample_Name
PCA_data<-as.data.frame(getM(gRatioSet.quantile))
#transpose the dataset (required for PCA)
data.pca<-t(PCA_data)
data.pca<-as.data.frame(data.pca)
##merge the file
data.pca_Final<-merge(Index_PCA, data.pca, by=0)
rownames(data.pca_Final)<-data.pca_Final$Row.names
pca.comp<-prcomp(data.pca_Final[,(ncol(Index_PCA)+2):ncol(data.pca_Final)])
pcaCharts=function(x) {
x.var <- x$sdev ^ 2
x.pvar <- x.var/sum(x.var)
par(mfrow=c(2,2))
plot(x.pvar,xlab="Principal component",
ylab="Proportion of variance", ylim=c(0,1), type='b')
plot(cumsum(x.pvar),xlab="Principal component",
ylab="Cumulative Proportion of variance",
ylim=c(0,1),
type='b')
screeplot(x)
screeplot(x,type="l")
par(mfrow=c(1,1))
}
pcaCharts(pca.comp)
png(file=paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_PCA.Charts.png"))
pcaCharts(pca.comp)
dev.off()## quartz_off_screen
## 23-Dimensional PCA
From the previous calculations, it is seens that only 2 principal components are necessary (accounting for >80% cumulative variance). Nonetheless, below is a 3-D PCA to ensure that all groups are characterize to higher-degree of stringency. Nevertheless, a racial difference could not be appreciated.
##Create a 3D-PCA for Inspection
library(plotly)
##Index
Index_PCA<-targets
rownames(Index_PCA)<-Index_PCA$Sample_Name
PCs<-merge(pca.comp$x, Index_PCA, by=0)
rownames(PCs)<-PCs$Row.names
PCs$Group <- as.factor(PCs$Sample_Group)
fig <- plot_ly(PCs, x = ~PC1, y = ~PC2, z = ~PC3, color = ~Sample_Group, text = ~paste('Sample_Name:', Sample_Name, '<br>Tissue:', Tissue, '<br>Outcome:', Outcome, '<br>Sex:', Sex))
fig <- fig %>% add_markers()
fig <- fig %>% layout(scene = list(xaxis = list(title = 'PC1'),
yaxis = list(title = 'PC2'),
zaxis = list(title = 'PC3')))
figCorrelation of Differential Gene Expression
# Format for Correlation
library(corrplot)
library(Hmisc)
Index_corr<-Index_PCA %>% dplyr::select(Sample_Group)
cor<-data.matrix(as.data.frame(getM(gRatioSet.quantile)))
cor.m<-rcorr(cor)
cor.r<-cor(cor)
paletteLength <- 100
myColor <- colorRampPalette(c("darkcyan", "white","firebrick", "white"))(paletteLength)
pdf(paste0("../2_Output/", COMPARISON, "/", COMPARISON,"_Correlation_heatmap.pdf"))
pheatmap(cor.r,
clustering_method = "ward.D2",
cluster_cols=T,
border_color="black",
cutree_cols = 2,
cluster_rows=T,
scale = "none",
show_colnames = F,
show_rownames = T,
color = myColor,
annotation_col = Index_corr)
dev.off()## pdf
## 3pheatmap(cor.r,
clustering_method = "ward.D2",
cluster_cols=T,
border_color="black",
cutree_cols = 2,
cluster_rows=T,
scale = "none",
show_colnames = F,
show_rownames = T,
color = myColor,
annotation_col = Index_corr)Differential Methylation of iPSCs (DCM vs. CON)
Using Minfi to compute differential expression
Owing to the apparent separation by patient Sample_Group, we chose to identify the CpG sites responsible for a Sample_Group-based epigenomic difference.
#Quantification and Differential Expression Analysis
RGSet<-minfi::read.metharray.exp(base = "../1_Input/IDAT", targets = targets, verbose = TRUE)
# sampleNames(RGSet)<-targets$Sample_Name
GRset.funnorm <- preprocessFunnorm(RGSet)
beta <- getBeta(GRset.funnorm)
M<-getM(GRset.funnorm)
Condition <- pData(GRset.funnorm)$Sample_Group
dmp <- dmpFinder(beta, pheno = Condition , type = "categorical")
DMPs<-merge(dmp, annoM450k, by= 0)
DMPs<-as.data.frame(DMPs)
rownames(DMPs)<-DMPs$Row.names
DMPs<-DMPs %>% dplyr::select(-Row.names)
#create an beta table
beta.table<-as.data.frame(t(beta))
beta.table$Col_ID<-rownames(beta.table)
beta_named<-merge(beta.table, targets, by = "Col_ID")
rownames(beta_named)<-beta_named$Sample_Name
beta_named<-beta_named %>% dplyr::select(-names(targets)) %>% t()
write.csv(beta_named, paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_beta.table.csv"))
#Add beta values to statistics
Results_dmp<-merge(DMPs, beta_named, by = 0)
#Calculate Average CpG Methylation by Sample_Group
library(dplyr)
library(matrixStats)
Results<-Results_dmp %>% replace(is.na(.), 0) %>% dplyr::mutate(
DCM_SD = rowSds(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="DCM"]])),
DCM_Mean = rowMeans(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="DCM"]])),
CON_SD = rowSds(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="CON"]])),
CON_Mean = rowMeans(as.matrix(Results_dmp[,targets$Sample_Name[targets$Sample_Group=="CON"]])),
Methylation.Diff=((DCM_Mean/CON_Mean)-1)*100)
rownames(Results)<-Results$Row.names
Results_dmp_p05<-filter(Results, pval<0.05)
Results_dmp_q05<-filter(Results, qval<0.05)
#########################################
#Identify Promoter-associated CpG Islands
library(tidyr)
PromCGI<-dplyr::filter(Results_dmp_p05, grepl("Island", Relation_to_Island), grepl("TSS", UCSC_RefGene_Group))
#Separate Gene Names into unique rows
PromCGI_sep<-PromCGI %>% mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>% unnest(UCSC_RefGene_Name) %>% distinct()
#Save a copy of the countData
library(openxlsx)
wb_countData<-createWorkbook()
addWorksheet(wb_countData, "Unfiltered")
writeData(wb_countData, "Unfiltered", Results, startCol = 1)
addWorksheet(wb_countData, "P_0.05")
writeData(wb_countData, "P_0.05", Results_dmp_p05, startCol = 1)
addWorksheet(wb_countData, "Q_0.05")
writeData(wb_countData, "Q_0.05", Results_dmp_q05, startCol = 1)
addWorksheet(wb_countData, "Promoter.CGI")
writeData(wb_countData, "Promoter.CGI", PromCGI_sep, startCol = 1)
saveWorkbook(wb_countData, file = paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_DMPs.xlsx"), overwrite = TRUE)Figure 2/3 B: Volcano Plot - DMPs
# Load packages
library(dplyr)
library(ggplot2)
library(ggrepel)
library(openxlsx)
Results<-read.xlsx(paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_DMPs.xlsx"), sheet = "Unfiltered")
#Read data from the web
Volcano_data = mutate(Results, sig=ifelse(Results$pval<0.05 & abs(Results$Methylation.Diff)>5, "P<0.05 and |Methylation| > 5%", "Not Sig"), minuslogpvalue = -log(pval), Methylation=Methylation.Diff)
#Split gene names for labelling
Volcano_data_split<-Volcano_data %>% mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>% unnest(UCSC_RefGene_Name) %>% distinct()
max(Volcano_data$minuslogpvalue, na.rm = TRUE)## [1] 33.01878# Results<-Results %>% filter(grepl("TSS", UCSC_RefGene_Group))
#plot the ggplot
p = ggplot(Volcano_data_split, aes(Methylation, minuslogpvalue)) +
theme(panel.background = element_rect("white", colour = "black", size=2),
panel.grid.major = element_line(colour = "gray50", size=.75),
panel.grid.minor = element_line(colour = "gray50", size=0.4),
legend.position = "none") +
geom_point(aes(fill=sig, size = minuslogpvalue),
colour="grey",
shape=21,
stroke = 0,
alpha = 8/10) +
labs(x=expression("Methylation Difference (%)"),
y=expression(-Log[10](P-value))) +
xlim(min(Volcano_data$Methylation, na.rm = TRUE),
max(Volcano_data$Methylation, na.rm = TRUE))+
ylim(-0,
max(20, na.rm = TRUE)) +
geom_hline(yintercept = 0, size = 1) +
geom_vline(xintercept=0, size=1)+
scale_fill_manual(values=c("grey", "darkgoldenrod2")) +
scale_size_continuous(range = c(.25, 4))
png(file = paste0("../2_Output/", COMPARISON, "/", COMPARISON, "Volcano.Plot.png"), units = "in" ,height = 4, width = 4, res=300)
p+
geom_text_repel(size = 2, data=top_n(filter(Volcano_data_split, pval<0.05, Methylation < 0, sig!="Not Sig"), 10, -Methylation), aes(label=UCSC_RefGene_Name)) +
geom_text_repel(size = 2, data=top_n(filter(Volcano_data_split, pval<0.05, Methylation > 0, sig!="Not Sig"), 10, Methylation), aes(label=UCSC_RefGene_Name))
dev.off()## quartz_off_screen
## 2p+
geom_text_repel(size = 2, data=top_n(filter(Volcano_data_split, pval<0.05, Methylation < 0, sig!="Not Sig"), 10, -Methylation), aes(label=UCSC_RefGene_Name)) +
geom_text_repel(size = 2, data=top_n(filter(Volcano_data_split, pval<0.05, Methylation > 0, sig!="Not Sig"), 10, Methylation), aes(label=UCSC_RefGene_Name))
Figure 2/3C-D: Distribution of Methylation by Genomic and CpG Annotation
The following figure illustrates the enrichment of differential methylation with respect to CpG-based and genomic annotations.
library(plotly)
library(dplyr)
library(tidyr)
library(stringr)
library(reshape2)
library(readxl)
library(kableExtra)
library(ComplexHeatmap)
library(openxlsx)
##Create a regional annotation matrix of the m450k array
Region_epic<-Results_dmp %>%
dplyr::select(Row.names, UCSC_RefGene_Group, Relation_to_Island)
Stage1<-Region_epic %>%
mutate(UCSC_RefGene_Group = strsplit(as.character(UCSC_RefGene_Group), ";")) %>%
unnest(UCSC_RefGene_Group)
Stage2<-Stage1 %>%
mutate(Relation_to_Island = strsplit(as.character(Relation_to_Island), ";")) %>%
unnest(Relation_to_Island)
Stage3<-distinct(Stage2)
Regional.Groups<-dplyr::group_by_(Stage3, "UCSC_RefGene_Group", "Relation_to_Island") %>%
tally()
Region.matrix<-Regional.Groups %>%
spread(Relation_to_Island, n)
Region.matrix<-Region.matrix %>%
dplyr::select(UCSC_RefGene_Group, OpenSea, N_Shelf, N_Shore, Island, S_Shore, S_Shelf)
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Region.matrix<-Region.matrix[c("TSS1500", "TSS200", "5'UTR", "1stExon", "Body", "3'UTR"),]
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Contour_3D_epic<-Region.matrix[,-1]
rownames(Contour_3D_epic)<-Region.matrix$UCSC_RefGene_Group
write.xlsx(Contour_3D_epic, paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_Contour.3D_EPIC.xlsx"), overwrite = TRUE)
##Create a regional annotation matrix of differentially-methylated positions
Region_p05<-Results_dmp_p05 %>% dplyr::select(Row.names, UCSC_RefGene_Group, Relation_to_Island)
Stage1<-Region_p05 %>% mutate(UCSC_RefGene_Group = strsplit(as.character(UCSC_RefGene_Group), ";")) %>% unnest(UCSC_RefGene_Group)
Stage2<-Stage1 %>% mutate(Relation_to_Island = strsplit(as.character(Relation_to_Island), ";")) %>% unnest(Relation_to_Island)
Stage3<-distinct(Stage2)
Regional.Groups<-dplyr::group_by_(Stage3, "UCSC_RefGene_Group", "Relation_to_Island") %>% tally()
Region.matrix<-Regional.Groups %>% spread(Relation_to_Island, n)
Region.matrix<-Region.matrix %>% dplyr::select(UCSC_RefGene_Group, OpenSea, N_Shelf, N_Shore, Island, S_Shore, S_Shelf)
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Region.matrix<-Region.matrix[c("TSS1500", "TSS200", "5'UTR", "1stExon", "Body", "3'UTR"),]
rownames(Region.matrix)<-Region.matrix$UCSC_RefGene_Group
Contour_3D<-Region.matrix[,-1]
rownames(Contour_3D)<-Region.matrix$UCSC_RefGene_Group
write.csv(Contour_3D, "../2_Output/Contour.3D_DMPs.p05.csv")
### Identify DMP Enrichment (IMPORTANT)
Enrichment_Region<-Contour_3D/Contour_3D_epic
Promoter_enr<-Enrichment_Region[rownames(Enrichment_Region)=="TSS200",] + Enrichment_Region[rownames(Enrichment_Region)=="TSS1500",]
rownames(Promoter_enr)<-"Promoter"
Enrichment_Region<-Enrichment_Region %>%
filter(!grepl("TSS", rownames(Enrichment_Region))) %>%
rbind(Promoter_enr, .) %>%
data.matrix()
paletteLength<-100
write.csv(Enrichment_Region, paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_Regional.Enrichment.csv"))
myColor <- colorRampPalette(c("dodgerblue4", "white", "brown4"))(paletteLength)
pheatmap(Enrichment_Region, color = myColor, cluster_rows = FALSE, cluster_cols = FALSE)
write.csv(Enrichment_Region, "DCM_vs_CON.csv")
##Make a Table of the CpG Methylation Distribution
Enrichment_Region %>% kable( align="c", booktabs=T,
caption="Methylation Distribution") %>%
kable_styling(latex_options=c("striped", "condensed", "repeat_header"))| OpenSea | N_Shelf | N_Shore | Island | S_Shore | S_Shelf | |
|---|---|---|---|---|---|---|
| Promoter | 0.3757536 | 0.4910442 | 0.3541229 | 0.2700382 | 0.3464998 | 0.4670582 |
| 5’UTR | 0.1994838 | 0.2071846 | 0.1971734 | 0.1366361 | 0.1928501 | 0.2000000 |
| 1stExon | 0.1786942 | 0.2201087 | 0.1871498 | 0.1369061 | 0.1739341 | 0.1986532 |
| Body | 0.1875371 | 0.1981427 | 0.1963882 | 0.1623604 | 0.2059241 | 0.1947722 |
| 3’UTR | 0.1970061 | 0.2608696 | 0.2306025 | 0.1763502 | 0.2155221 | 0.2440087 |
write.xlsx(Enrichment_Region, paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_DMP.Enrichment_3D.xlsx"), overwrite = T)
color <- colorRampPalette(c("grey", "orange", "red"))
t <- list(
family = "times",
size = 16,
color = "black")
x_axis<-list(title = 'CpG Region',
type="category",
zeroline=TRUE,
showline=TRUE,
zerolinewidth = 4,
zerolinecolor="darkgrey",
linecolor="darkgrey",
linewidth=4,
titlefont=t,
tickfont=t)
y_axis<-list(title = 'Gene Region',
type="category",
zeroline=TRUE,
showline=TRUE,
zerolinewidth = 4,
zerolinecolor="darkgrey",
linecolor="darkgrey",
linewidth=4,
titlefont=t,
tickfont=t)
z_axis<-list(title = 'Number of DMPs',
zerolinewidth = 4,
zerolinecolor="darkgrey",
linecolor="darkgrey",
linewidth=4,
titlefont=t,
tickfont=t)
q<-plot_ly(z=~Enrichment_Region, colors=color(10),
text=as.character(rownames(Enrichment_Region))) %>% add_surface() %>%
layout(scene = list(xaxis = x_axis, yaxis = y_axis, zaxis = z_axis))
q #must comment out for PDF generation via knitr (Pandoc).Figure 2/3E: Heatmap and Hierarchical Clustering of Differential Methylation (P < 0.05)
Due to the prominent signature of CpG Island-associated promoter methylation in iPSCs exposed to serum for failing and non-failing patients, we examined all DMPs present within this region via heatmap.
library(ComplexHeatmap)
library(dplyr)
##Import Data Matrix
# betaHM<-read.csv("../1_Input/EPIC.betaValues.csv", row.names = 1)
## Filters to Apply to DMP
pvalue_threshold=0.05
METHYLATION=0
# DMP_location="Island"
Gene_region="TSS"
Samples<-AnnoTargets$Sample_Name
##Filter Differential Methylation Data
DMP.p05<-Results %>% filter(pval<pvalue_threshold)
DMP.p05<-DMP.p05 %>% dplyr::select(Row.names,
Methylation.Diff,
pval,
qval,
Relation_to_Island,
UCSC_RefGene_Group,
chr,
pos,
matches(Samples)) %>%
filter(abs(Methylation.Diff)>METHYLATION)
DMP.p05.Region<-DMP.p05 %>%
# filter(grepl(DMP_location, Relation_to_Island)) %>%
filter(grepl(Gene_region, UCSC_RefGene_Group)) %>%
dplyr::select(matches(AnnoTargets$Sample_Name)) %>%
data.matrix()
nrow(DMP.p05.Region)## [1] 22653#Import the Index File
LVAD_Counts_Data <- targets
rownames(LVAD_Counts_Data)<-targets$Sample_Name
Index<-LVAD_Counts_Data %>% dplyr::select(Sample_Group)
Index<-as.data.frame(Index)
paletteLength <- 100
ann_colors = list(Sample_Group = c(DCM="darkcyan", CON="darkgray"), Outcome = c(Bad = "firebrick2", Good = "darkgoldenrod2", CON = "black"))
myColor <- colorRampPalette(c("dodgerblue4", "white", "goldenrod2"))(paletteLength)
pheatmap::pheatmap(DMP.p05.Region, scale="row",
cluster_cols = TRUE,
cluster_rows = TRUE,
#breaks = myBreaks,
cutree_cols = 2,
cutree_rows = 2,
angle_col = 45,
fontsize_col = 8,
color = myColor,
show_rownames = FALSE,
show_colnames = F,
border_color = NA,
annotation_col = Index,
annotation_colors=ann_colors,
legend = F,
annotation_legend = F,
filename = paste0("../2_Output/", COMPARISON, "/", COMPARISON, "_", Gene_region,".heatmap.pdf"),
width = 5,
height = 5)
pheatmap::pheatmap(DMP.p05.Region, scale="row",
cluster_cols = TRUE,
cluster_rows = TRUE,
#breaks = myBreaks,
cutree_cols = 2,
cutree_rows = 2,
angle_col = 45,
fontsize_col = 8,
color = myColor,
show_rownames = FALSE,
border_color = NA,
annotation_col = Index,
annotation_colors=ann_colors)Figure 4: Combined Analysis - Biopsy and iPSC
library(openxlsx)
library(dplyr)
library(tidyr)
library(ComplexHeatmap)
library(minfi)
NUMBER = 20
STAT = 0.001
#Index
AnnoTargets<-read.metharray.sheet(base="../1_Input/IDAT", pattern=".csv")## [1] "../1_Input/IDAT/SampleSheet.csv"rownames(AnnoTargets)<-AnnoTargets$Sample_Name
Index_combined<-AnnoTargets %>% dplyr::select(Sample_Group, Tissue)
#iPSC Data
DMPs_iPSC<-read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
iPSC_stats<-DMPs_iPSC %>% dplyr::select(Methylation_iPSC = Methylation.Diff, pval_iPSC = pval, adj.P.Val_iPSC = qval, Name:Regulatory_Feature_Group)
#biopsies
DMPs_heart<-read.xlsx("../2_Output/heart_DCM_vs_CON/heart_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
heart_stats<-DMPs_heart %>% dplyr::select(Methylation_heart = Methylation.Diff, pval_heart = pval, adj.P.Val_heart = qval, Name:Regulatory_Feature_Group)
heart_index<-AnnoTargets %>% dplyr::filter(Tissue=="heart") %>% dplyr::select(Tissue, Sample_Group)
#Beta
beta_all<-read.csv("../1_Input/beta_all.csv", row.names = 1)
#combine data
Combined_DMPs<-inner_join(iPSC_stats, heart_stats)
Combined_DMPs_Separated<-Combined_DMPs %>% mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>% unnest(UCSC_RefGene_Name) %>% distinct() %>% merge(., beta_all, by.x = "Name", by.y = 0)
write.xlsx(Combined_DMPs_Separated, "../2_Output/Combined_DMPs.xlsx")
# Select only co-methylated positions (iPSC and heart)
Combined_together<-Combined_DMPs_Separated %>% filter(Methylation_iPSC>0 & Methylation_heart>0 | Methylation_iPSC<0 & Methylation_heart<0) %>% arrange(desc(Methylation_iPSC)) %>% filter(pval_iPSC < STAT) %>% arrange(pval_iPSC) %>% tidyr::separate(., "UCSC_RefGene_Group", "UCSC_RefGene_Group", sep = ";", extra = "drop")
##Add RNA-sequencing Data
iPSC_RNA<-read.xlsx("../RNA/2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DESeq2.xlsx", sheet = "P_0.05") %>% dplyr::select(UCSC_RefGene_Name=gene_name, log2FoldChange_RNA=log2FoldChange, pvalue_RNA=pvalue)
Combined_together<-left_join(Combined_together, iPSC_RNA, by = "UCSC_RefGene_Name")
# Combined_together<-merge(Combined_together, beta_all, by.x = "Name", by.y = 0)
rownames(Combined_together)<-make.unique(Combined_together$UCSC_RefGene_Name, sep = ".")
#Create heatmap matrices and annotation
heart_hm<-Combined_together %>% dplyr::select(contains("NF") | contains("biopsy")) %>% data.matrix()
heart_index<-AnnoTargets %>% dplyr::filter(Tissue=="heart") %>% dplyr::select(Tissue, Sample_Group)
iPSC_hm<-Combined_together %>% dplyr::select(contains("cells") & contains("co"),contains("cells") & contains("go"), contains("cells") & contains("bo")) %>% data.matrix()
iPSC_index<-AnnoTargets %>% dplyr::filter(Tissue=="iPSC") %>% dplyr::select(Tissue, Sample_Group)
write.xlsx(Combined_together, "../2_Output/Overlapping.DMPs_iPSC.Biopsy.xlsx", overwrite = T)
# Venn Diagram
library(VennDiagram)
futile.logger::flog.threshold(futile.logger::ERROR, name = "VennDiagramLogger")## NULLx<-list(iPSC = DMPs_iPSC$Name, heart = DMPs_heart$Name)
venn.diagram(x,fill = c("darkgray", "firebrick2"), alpha = c(0.75, 0.75), lty = 'blank', filename = "../2_Output/Overlapping_DMPs_iPSC.Biopsy.png", na = "remove")## [1] 1# Heatmap
ann_colors = list(Sample_Group = c(DCM="#1b9e77", CON = "goldenrod2"), Tissue = c(heart = "coral2", iPSC = "darkgray"))
paletteLength <- 100
myColor <- colorRampPalette(c("dodgerblue4", "white", "gold2"))(paletteLength)
#iPSC
ha = rowAnnotation(foo = anno_mark(at = c(1:10), labels = Combined_together$UCSC_RefGene_Name[1:10]))
#Create a filter
# Annotate<-Combined_together %>% filter(log2FoldChange_RNA!="NA")
# ha = rowAnnotation(foo = anno_mark(at = which(Combined_together$log2FoldChange_RNA!="NA"), labels=Annotate$UCSC_RefGene_Name,
# labels_gp = gpar(fontsize = 10), padding = unit(1, "mm")))
heatmap_iPSC<-ComplexHeatmap::pheatmap(iPSC_hm, scale="row",
name = "iPSC\n Z-score",
cluster_cols = F,
cluster_rows = T,
cutree_rows = 2,
fontsize_col = 8,
color = myColor,
annotation_names_col = FALSE,
show_colnames = F,
show_rownames = F,
border_color = NA,
annotation_colors = ann_colors,
annotation_col = iPSC_index,
border = TRUE)
heatmap_iPSC
#heart
heatmap_heart<-ComplexHeatmap::pheatmap(heart_hm,
name = "Biopsy\n Z-score",
scale = "row",
cluster_cols = F,
cluster_rows = T,
cutree_rows = 2,
fontsize_col = 8,
color = myColor,
show_rownames = F,
show_colnames = F,
border_color = NA,
annotation_names_col = FALSE,
annotation_colors = ann_colors,
annotation_col = heart_index,
border = TRUE)
heatmap_heart
RNAColor <- colorRampPalette(c("dodgerblue4", "white", "gold2"))(paletteLength)
iPSC_RNA<-Heatmap(Combined_together$log2FoldChange_RNA,
name = "DEG",
na_col = "white",
col = RNAColor,
show_column_names = T,
right_annotation = ha,
width = unit(5, "mm"))
Annotation_CpG<-Heatmap(Combined_together$Relation_to_Island,
name = "CpG",
col = c("S_Shelf" = "deepskyblue3", "S_Shore" = "deepskyblue", "Island" = "blanchedalmond", "N_Shore" = "deepskyblue", "N_Shelf" = "deepskyblue3", "OpenSea" = "deepskyblue4"),
column_names_rot = 45,
column_names_gp = gpar(fontsize = 10),
width = unit(5, "mm"))
Annotation_Gene<-Heatmap(Combined_together$UCSC_RefGene_Group,
name = "Location",
col = c("TSS1500" = "azure4", "TSS200" = "azure3", "5'UTR" = "azure2", "1stExon" = "darkslategray2", "Body" = "darkslategray3"),
right_annotation = ha,
column_names_rot = 45,
column_names_gp = gpar(fontsize = 10),
width = unit(5, "mm"))
heatmap_heart + heatmap_iPSC + Annotation_CpG + Annotation_Gene
pdf(file="../2_Output/Figure_4C_Conserved.DMPs.pdf", height = 7, width = 8, onefile = F)
heatmap_heart + heatmap_iPSC + Annotation_CpG + Annotation_Gene
dev.off()## quartz_off_screen
## 2Figure 5A: Combined-Omics
library(openxlsx)
library(dplyr)
library(tidyr)
library(ComplexHeatmap)
library(minfi)
NUMBER = 20
STAT = 0.01
#Index
AnnoTargets<-read.metharray.sheet(base="../1_Input/IDAT", pattern=".csv")## [1] "../1_Input/IDAT/SampleSheet.csv"rownames(AnnoTargets)<-AnnoTargets$Sample_Name
Index_combined<-AnnoTargets %>% dplyr::select(Sample_Group, Tissue)
#iPSC Data
DMPs_iPSC<-read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
iPSC_stats<-DMPs_iPSC %>% dplyr::select(Methylation_iPSC = Methylation.Diff, pval_iPSC = pval, adj.P.Val_iPSC = qval, Name:Regulatory_Feature_Group)
#biopsies
DMPs_heart<-read.xlsx("../2_Output/heart_DCM_vs_CON/heart_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
DMPs_heart$Relation_to_Island<-factor(DMPs_heart$Relation_to_Island, levels = c("OpenSea", "N_Shelf", "N_Shore", "Island", "S_Shore", "S_Shelf"))
heart_stats<-DMPs_heart %>% dplyr::select(Methylation_heart = Methylation.Diff, pval_heart = pval, adj.P.Val_heart = qval, Name:Regulatory_Feature_Group)
heart_index<-AnnoTargets %>% dplyr::filter(Tissue=="heart") %>% dplyr::select(Tissue, Sample_Group)
#Beta
beta_all<-read.csv("../1_Input/beta_all.csv", row.names = 1)
#combine data
Combined_DMPs<-inner_join(iPSC_stats, heart_stats)
#Clean data
Combined_DMPs_Separated<-Combined_DMPs %>%
mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>%
unnest(UCSC_RefGene_Name) %>%
distinct() %>%
merge(., beta_all, by.x = "Name", by.y = 0)
# Select only co-methylated positions (iPSC and heart)
Combined_together<-Combined_DMPs_Separated %>%
filter(Methylation_iPSC>0 & Methylation_heart>0 | Methylation_iPSC<0 & Methylation_heart<0) %>%
filter(pval_iPSC < STAT) %>%
tidyr::separate(., "UCSC_RefGene_Group", "UCSC_RefGene_Group", sep = ";", extra = "drop") %>%
dplyr::mutate(UCSC_RefGene_Group=factor(UCSC_RefGene_Group, levels = c("Intergenic","TSS1500", "TSS200", "5'UTR", "1stExon", "Body", "3'UTR"))) %>%
dplyr::mutate(Direction=ifelse(Methylation_iPSC>0, "UP", "DOWN")) %>%
arrange(Relation_to_Island) %>%
arrange(UCSC_RefGene_Group) %>%
arrange(Direction)
##Add RNA-sequencing Data
iPSC_RNA<-read.xlsx("../RNA/2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DESeq2.xlsx", sheet = "P_0.05") %>%
dplyr::select(UCSC_RefGene_Name=gene_name, log2FoldChange_RNA=log2FoldChange, pvalue_RNA=pvalue)
Combined_together<-left_join(Combined_together, iPSC_RNA, by = "UCSC_RefGene_Name")
# Combined_together<-merge(Combined_together, beta_all, by.x = "Name", by.y = 0)
rownames(Combined_together)<-make.unique(Combined_together$UCSC_RefGene_Name, sep = ".")
#Create heatmap matrices and annotation
heart_hm<-Combined_together %>% dplyr::select(contains("NF") | contains("biopsy")) %>% data.matrix()
heart_index<-AnnoTargets %>% dplyr::filter(Tissue=="heart") %>% dplyr::select(Tissue, Sample_Group)
iPSC_hm<-Combined_together %>% dplyr::select(contains("cells") & contains("co"),contains("cells") & contains("go"), contains("cells") & contains("bo")) %>% data.matrix()
iPSC_index<-AnnoTargets %>% dplyr::filter(Tissue=="iPSC") %>% dplyr::select(Tissue, Sample_Group)
write.xlsx(Combined_together, "../2_Output/Overlapping.DMPs_iPSC.Biopsy.xlsx", overwrite = T)
# Venn Diagram
library(VennDiagram)
futile.logger::flog.threshold(futile.logger::ERROR, name = "VennDiagramLogger")## NULLx<-list(iPSC = DMPs_iPSC$Name, heart = DMPs_heart$Name)
venn.diagram(x,fill = c("darkgray", "firebrick2"), alpha = c(0.75, 0.75), lty = 'blank', filename = "../2_Output/Overlapping_DMPs_iPSC.Biopsy.png", na = "remove")## [1] 1# Heatmap
ann_colors = list(Sample_Group = c(DCM="lightseagreen", CON = "darkgray"), Tissue = c(heart = "coral2", iPSC = "lightskyblue3"))
paletteLength <- 100
myColor <- colorRampPalette(c("dodgerblue4", "white", "goldenrod2"))(paletteLength)
# Filter out DMPs lacking associated DEGs
Annotate<-Combined_together %>% filter(log2FoldChange_RNA!="NA")
write.xlsx(Annotate, "../2_Output/DMPs.w.DEGs_P05.xlsx", overwrite = T)
#Export genes as a bed file (for motif enrichment)
library(bedr)
bed_candidates<-Annotate %>% transmute(chr=chr, start=pos-20, end=pos+20, Name)
bed <- bed_candidates[,c('chr', 'start', 'end', 'Name')]
# Test<-get.fasta(bed, fasta = "../2_Output/GRCh37.primary_assembly.genome.fa")
write.table(bed, "../2_Output/DMR.DEG_motif.bed",quote=FALSE,
row.names=FALSE,col.names=FALSE,sep="\t")
# Add Annotation containing DEGs
ha = rowAnnotation(foo = anno_mark(at = which(Combined_together$log2FoldChange_RNA!="NA"), labels=Annotate$UCSC_RefGene_Name,
labels_gp = gpar(fontsize = 5), padding = unit(1, "mm")))
heatmap_iPSC<-ComplexHeatmap::pheatmap(iPSC_hm, scale="row",
name = "iPSC\n Z-score",
cluster_cols = F,
cluster_rows = F,
# cutree_rows = 2,
fontsize_col = 8,
color = myColor,
annotation_names_col = FALSE,
show_colnames = F,
show_rownames = F,
border_color = NA,
annotation_colors = ann_colors,
annotation_col = iPSC_index,
border = TRUE,
breaks = c(-2, 0, 2),
use_raster = F,
legend = F)
heatmap_iPSC
#heart
heatmap_heart<-ComplexHeatmap::pheatmap(heart_hm,
name = "Methylation\n (Z-score)",
scale = "row",
cluster_cols = F,
cluster_rows = F,
# cutree_rows = 2,
fontsize_col = 8,
color = myColor,
show_rownames = F,
show_colnames = F,
border_color = NA,
annotation_names_col = FALSE,
annotation_colors = ann_colors,
annotation_col = heart_index,
border = TRUE,
breaks = c(-2, 0, 2),
use_raster = F)
heatmap_heart
library(circlize)
RNAColor = colorRamp2(c(-2, 0, 2), c("dodgerblue4", "white", "firebrick2"))
iPSC_RNA<-Heatmap(Combined_together$log2FoldChange_RNA,
name = "iPSC DEGs",
na_col = "white",
col = RNAColor,
show_column_names = T,
right_annotation = ha,
width = unit(5, "mm"),
column_names_rot = 45,
column_names_gp = gpar(fontsize = 10))
Annotation_CpG<-Heatmap(Combined_together$Relation_to_Island,
name = "CpG",
col = c("S_Shelf" = "deepskyblue3", "S_Shore" = "deepskyblue", "Island" = "blanchedalmond", "N_Shore" = "deepskyblue", "N_Shelf" = "deepskyblue3", "OpenSea" = "deepskyblue4"),
column_names_rot = 45,
column_names_gp = gpar(fontsize = 10),
width = unit(5, "mm"))
Annotation_Gene<-Heatmap(Combined_together$UCSC_RefGene_Group,
name = "Location",
col = c("TSS1500" = "azure4", "TSS200" = "azure3", "5'UTR" = "azure2", "1stExon" = "darkslategray2", "Body" = "darkslategray3", "3'UTR"="black"),
column_names_rot = 45,
column_names_gp = gpar(fontsize = 10),
width = unit(5, "mm"))
Figure_5A<-heatmap_heart + heatmap_iPSC + Annotation_CpG + Annotation_Gene + iPSC_RNA
Figure_5A
pdf(file="../2_Output/Figure_5_DMPs_and_DEGs.pdf", height = 7, width = 6.5, onefile = F)
Figure_5A
dev.off()## quartz_off_screen
## 2png(file="../2_Output/Figure_5_DMPs_and_DEGs.png", units = "in",height = 7, width = 6.5, res = 300)
Figure_5A
dev.off()## quartz_off_screen
## 2Correlate Gene Expression with DNA Methylation
library(openxlsx)
library(dplyr)
library(tidyr)
library(Hmisc)
library(stringr)
#Import the differential data
RNA.Counts<-read.xlsx(paste0("../RNA/2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DESeq2.xlsx"), sheet = "P_0.05")
colnames(RNA.Counts)<-paste0("RNA_",colnames(RNA.Counts))
CpGs<-read.xlsx(paste0("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx"), sheet = "P_0.05")
colnames(CpGs)<-paste0("Methyl_", colnames(CpGs))
# align methyl and RNAs, and separate into different tables
idx2 <- sapply(RNA.Counts$RNA_gene_name, grep, CpGs$Methyl_UCSC_RefGene_Name) # filters
idx1 <- sapply(seq_along(idx2), function(i) rep(i, length(idx2[[i]])))
test<-cbind(RNA.Counts[unlist(idx1),,drop=F], CpGs[unlist(idx2),,drop=F])
rownames(test)<-make.unique(test$Methyl_Row.names)
RNAs<-test %>% dplyr::select(RNA_A1:RNA_C10)
RNA_cor<-RNAs
Methyls<-test %>% dplyr::select(Methyl_A1_cells_bo:Methyl_C7_cells_co)
Methyl_names<-gsub(pattern = "Methyl_", replacement = "", x = colnames(Methyls))
Methyl_names<-str_remove(Methyl_names, '_.*')
Methyl_cor<-Methyls
colnames(Methyl_cor)<-Methyl_names
RNA_names<-gsub(pattern = "RNA_", replacement = "", x = colnames(RNAs))
colnames(RNA_cor)<-RNA_names
#Ensure that the order and columns match exactly
col2keep = intersect(colnames(RNA_cor), colnames(Methyl_cor))
# Methyl_cor = Methyl_cor[,order(match(colnames(Methyl_cor),col2keep))]
Methyl_cor = Methyl_cor[,col2keep]
# RNAs = RNA_cor[,order(match(Methyl_cor, col2keep))]
#
# Methyl_test = RNA_cor[,order(match(colnames(RNA_cor),col2keep))]
RNA_cor = RNA_cor[,col2keep]
#
tRNAs_norm<-scale(t(RNA_cor))
tMethyls_norm<-scale(t(Methyl_cor))
corr.spearman_p<-0
corr.spearman_r<-0
for (i in 1:ncol(tMethyls_norm)) {
corr.test = rcorr(tRNAs_norm[,i], tMethyls_norm[,i], type = "spearman")
corr.spearman_p[i] = corr.test$P[1,2]
corr.spearman_r[i] = corr.test$r[1,2]
}
Final<-cbind(test, corr.spearman_p, corr.spearman_r) %>% dplyr::select(-contains(".x"), -contains(".y")) %>% distinct() %>% arrange(corr.spearman_p)
Final_corr.sig<-Final %>% filter(corr.spearman_p<0.05)
Final_all.sig<-Final %>% filter(corr.spearman_p<0.1, RNA_pvalue<0.05, Methyl_pval<0.05)
#
wb_correlation<-createWorkbook()
addWorksheet(wb_correlation, "Unfiltered")
writeData(wb_correlation, "Unfiltered", Final, startCol = 1)
addWorksheet(wb_correlation, "All Significant")
writeData(wb_correlation, "All Significant", Final_all.sig, startCol = 1)
addWorksheet(wb_correlation, "Correlation Significance")
writeData(wb_correlation, "Correlation Significance", Final_corr.sig, startCol = 1)
saveWorkbook(wb_correlation, file = paste0("../2_Output/iPSC_DMP.DEG_correlation.xlsx"), overwrite = TRUE)DMP-RNA Correlation
This tests the correlation between DNA methylation and gene expression in iPSCs.
library(ggplot2)
library(ggpubr)
library(ggrepel)
options(ggrepel.max.overlaps = Inf)
DMPs_iPSC<-read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
iPSC_RNA<-read.xlsx("../RNA/2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DESeq2.xlsx", sheet = "P_0.05") %>% dplyr::select(UCSC_RefGene_Name=gene_name, log2FoldChange_RNA=log2FoldChange, pvalue_RNA=pvalue)
iPSC_Combined<-left_join(DMPs_iPSC, iPSC_RNA, by = "UCSC_RefGene_Name")
Plot<-iPSC_Combined #%>% filter(Relation_to_Island=="Island",UCSC_RefGene_Group=="TSS1500" | UCSC_RefGene_Group=="TSS200" | UCSC_RefGene_Group=="5'UTR") %>% na.omit()
ggplot(Plot, aes(x=Methylation.Diff, y=log2FoldChange_RNA)) +
geom_point()+
# geom_smooth(method=lm) +
geom_rug() +
geom_hline(yintercept = 0, size = 1) +
geom_vline(xintercept=0, size=1) +
# geom_text_repel(data=Plot, aes(label=UCSC_RefGene_Name), show_guide = F) +
stat_cor(method = "spearman") +
theme_light()
Candidate Gene-Methylation Correlation
ifelse(!dir.exists(file.path(paste0("../2_Output/Candidates/"))), dir.create(file.path(paste0("../2_Output/Candidates/"))), FALSE)## [1] FALSElibrary(ggplot2)
library(ggrepel)
library(stringr)
library(gridExtra)
library(dplyr)
library(ggpubr)
GENE=c("DZIP1L") #, "ALG2", "LRP1", "QSOX1", "KANK2", "COL5A1"
#Index
Index_corr<-read.csv("../RNA/1_Input/colData.csv", row.names = 1)
Index<-Index_corr %>% data.frame()
# import DNA methylation data
DMPs_iPSC<-openxlsx::read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
DMPs<-DMPs_iPSC %>% dplyr::select(UCSC_RefGene_Name, Name, contains("_co") | contains("_bo") | contains("go"))
colnames(DMPs)[3:ncol(DMPs)]<-str_remove(colnames(DMPs)[3:ncol(DMPs)], '_.*')
DMP_Candidate<-DMPs %>% filter(grepl(GENE, UCSC_RefGene_Name) | grepl(GENE, Name)) %>% dplyr::select(-UCSC_RefGene_Name, -Name)
CPG_CANDIDATES=rownames(DMP_Candidate)
tDMP_Candidate<-scale(t(DMP_Candidate))
colMeans(tDMP_Candidate)## cg09151521 cg24585731
## -4.940348e-17 -7.424616e-16# import RNA-seq data
iPSC_RNA<-openxlsx::read.xlsx("../RNA/2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DESeq2.xlsx", sheet = "Unfiltered")
DEG_Candidate<-iPSC_RNA %>% filter(grepl(GENE, gene_name)) %>% dplyr::select(A1:C10)
DEG_Candidate<-scale(t(DEG_Candidate))
# merge DNA methylation and RNA-sequencing data
iPSC_Combined<-merge(tDMP_Candidate, DEG_Candidate, by = 0) %>% dplyr::rename(DEG=V1)
#Add Index
iPSC_Combined<-merge(iPSC_Combined, Index_corr, by.x = "Row.names", by.y=0)
openxlsx::write.xlsx(iPSC_Combined, "../2_Output/Candidates/Candidate.xlsx")
plotlist = list()
for(i in 1:length(CPG_CANDIDATES)){
Graph_candidate<-ggplot(iPSC_Combined, aes(x=iPSC_Combined[,CPG_CANDIDATES[i]], y=DEG)) +
geom_point()+
labs(title=paste0(GENE, ": ", CPG_CANDIDATES[i]),
x ="CpG Methylation (beta)", y = "Gene Expression (Counts)") +
geom_smooth(method=lm) +
geom_rug() +
geom_hline(yintercept = 0, size = 1) +
geom_vline(xintercept=0, size=1) +
geom_text_repel(data=iPSC_Combined, aes(label=Row.names), show.legend = F,colour = "darkgray") +
stat_cor(method = "spearman") +
theme_light()
pdf(file=paste0("../2_Output/Candidates/", GENE, "_", CPG_CANDIDATES[i], "_barplot.pdf"), width = 5, height =4)
print(Graph_candidate)
dev.off()
plotlist[[i]]=Graph_candidate
}
t<-marrangeGrob(grobs = plotlist, legend, nrow=1, ncol=1, top="Main Title")
ggsave(paste0("../2_Output/Candidates/Barplots.pdf"), t, width = 6, height = 7)library("CMplot")
library(dplyr)
library(stringr)
library(magrittr)
DMPs_iPSC<-read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T) %>% mutate(UCSC_RefGene_Name = strsplit(as.character(UCSC_RefGene_Name), ";")) %>% unnest(UCSC_RefGene_Name) %>% distinct()
DMPs_iPSC$UCSC_RefGene_Name<-make.unique(DMPs_iPSC$UCSC_RefGene_Name, sep = ".")
rownames(DMPs_iPSC)<-DMPs_iPSC$UCSC_RefGene_Name
manhattan<-DMPs_iPSC %>% transmute(SNP=make.unique(DMPs_iPSC$UCSC_RefGene_Name), chr, pos, minuslogpval=-log10(pval), Methylation.Diff) %>% transform(chr=str_replace(chr,"chr",""))
manhattan<-manhattan %>% filter(minuslogpval!="NA")
manhattan$pval<-as.integer(manhattan$minuslogpval)
# manhattan$chr<-as.integer(manhattan$chr)
manhattan$pos<-as.numeric(manhattan$pos)
str(manhattan)## 'data.frame': 24205 obs. of 6 variables:
## $ SNP : chr "RBL2" "CNBP" "MRPS25" "TMEM182" ...
## $ chr : chr "16" "3" "3" "2" ...
## $ pos : num 5.35e+07 1.29e+08 1.51e+07 1.03e+08 5.66e+07 ...
## $ minuslogpval : num 1.76 1.58 1.42 2.21 1.34 ...
## $ Methylation.Diff: num 3.464 11.183 -18.353 -0.854 11.305 ...
## $ pval : int 1 1 1 2 1 1 1 1 1 1 ...write.csv(manhattan, "manhattan.csv")
#create genomic labels
SNPs <- manhattan[manhattan$minuslogpval > 5, 1]
genes <- SNPs
# CMplot(manhattan, plot.type="m",col=c("grey30","grey60"), LOG10=F, highlight = SNPs, cex = .3,threshold = (5),highlight.text.cex = 5, highlight.text=SNPs, highlight.col="darkcyan", amplify=TRUE,bin.size=1e6, chr.den.col=c("dodgerblue4", "white", "gold2"),file="jpg", memo="", dpi=300, file.output=TRUE, verbose=TRUE, width=5.5, height=5)Top Candidates (DMP-DEGs)
library(openxlsx)
heart_DMPs<-read.xlsx("../2_Output/heart_DCM_vs_CON/heart_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05") %>% dplyr::select(Name, UCSC_RefGene_Name, pval_heart=pval, Methylation.Diff_heart=Methylation.Diff)
iPSC_DMPs<-read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05") %>% dplyr::select(Name, UCSC_RefGene_Name, pval_iPSC=pval, Methylation.Diff_iPSC=Methylation.Diff)
#Select co-methylated DMPs
CoDMPs<-inner_join(heart_DMPs, iPSC_DMPs)Meder Validation
library(openxlsx)
library(dplyr)
#Import Meder (2017) Validation data
Meder_heart<-openxlsx::read.xlsx("../3_Results/Validation_Meder/Overlapping.DMPs_iPSC.Biopsy_DCM_Mederlab_20220112.xlsx", sheet = "heart") %>% filter(pvalue<0.05) %>% dplyr::select(Name=CpG, UCSC_RefGene_Name, pval_Meder.heart=pvalue, fold.change_Meder.heart=fold.change)
Meder_blood<-openxlsx::read.xlsx("../3_Results/Validation_Meder/Overlapping.DMPs_iPSC.Biopsy_DCM_Mederlab_20220112.xlsx", sheet = "blood") %>% filter(pvalue<0.05) %>% dplyr::select(Name=CpG, UCSC_RefGene_Name, pval_Meder.blood=pvalue, fold.change_Meder.blood=fold.change)
#Import data from this experiment
Oeing_DMPs<-openxlsx::read.xlsx("../2_Output/Overlapping.DMPs_iPSC.Biopsy.xlsx")
Oeing_DMPs.DEGs<-openxlsx::read.xlsx("../2_Output/DMPs.w.DEGs_P05.xlsx")
#Overlap between Meder-heart and Oeing
Heart_Validated<-inner_join(Oeing_DMPs, Meder_heart, by = "Name") %>% dplyr::select(chr, pos, Name, UCSC_RefGene_Name=UCSC_RefGene_Name.x, Relation_to_Island, UCSC_RefGene_Group, Methylation_heart, pval_heart, Methylation_iPSC, pval_iPSC, log2FoldChange_RNA, pvalue_RNA) %>% arrange(-abs(Methylation_iPSC))
Heart_Validated.DEG<-Heart_Validated %>% filter(pvalue_RNA<0.05)
Blood_Validated<-inner_join(Oeing_DMPs, Meder_blood, by = "Name") %>% dplyr::select(chr, pos, Name, UCSC_RefGene_Name=UCSC_RefGene_Name.x, Relation_to_Island, UCSC_RefGene_Group, Methylation_heart, pval_heart, Methylation_iPSC, pval_iPSC, log2FoldChange_RNA, pvalue_RNA) %>% arrange(-abs(Methylation_iPSC))
Blood_Validated.DEG<-Blood_Validated %>% filter(pvalue_RNA<0.05)
ALL_Validated<-inner_join(Heart_Validated, Blood_Validated)
All_Validated.DEG<-ALL_Validated %>% filter(pvalue_RNA<0.05)
All_Validated.DEG$Group<-"ALL"
#VENN
Blood.valid_ONLY<-anti_join(Blood_Validated.DEG, All_Validated.DEG)
Blood.valid_ONLY$Group<-"Blood_ONLY"
Heart.valid_ONLY<-anti_join(Heart_Validated.DEG, All_Validated.DEG)
Heart.valid_ONLY$Group<-"Heart_ONLY"
CoDMP<-anti_join(Oeing_DMPs.DEGs, All_Validated.DEG) %>% anti_join(., Blood_Validated.DEG) %>% anti_join(., Heart_Validated.DEG)
CoDMP$Group<-"Unvalidated"
Venn.table<-full_join(Blood.valid_ONLY, Heart.valid_ONLY) %>% full_join(., CoDMP) %>% full_join(., All_Validated.DEG)
wb_correlation<-createWorkbook()
addWorksheet(wb_correlation, "Heart_Validated")
writeData(wb_correlation, "Heart_Validated", Heart_Validated, startCol = 1)
addWorksheet(wb_correlation, "Heart_Validated.DEGs")
writeData(wb_correlation, "Heart_Validated.DEGs", Heart_Validated.DEG, startCol = 1)
addWorksheet(wb_correlation, "Blood_Validated")
writeData(wb_correlation, "Blood_Validated", Blood_Validated, startCol = 1)
addWorksheet(wb_correlation, "Blood_Validated.DEGs")
writeData(wb_correlation, "Blood_Validated.DEGs", Blood_Validated.DEG, startCol = 1)
addWorksheet(wb_correlation, "ALL_Validated")
writeData(wb_correlation, "ALL_Validated", ALL_Validated, startCol = 1)
addWorksheet(wb_correlation, "ALL_Validated.DEGs")
writeData(wb_correlation, "ALL_Validated.DEGs", All_Validated.DEG, startCol = 1)
addWorksheet(wb_correlation, "Venn.Table")
writeData(wb_correlation, "Venn.Table", Venn.table, startCol = 1)
saveWorkbook(wb_correlation, file = paste0("../3_Results/Validation_Meder/Validation_Meder.xlsx"), overwrite = TRUE)
#Heart
bed_heart<-Heart_Validated %>% dplyr::select(chr, pos, Methylation_iPSC) %>% transmute(seqnames=chr, start=pos-10, end=pos+10, width = 21, strand = "*", deltaMeth=Methylation_iPSC)
bed_mr.heart<-as(bed_heart, "GRanges")
#Export genes as a bed file (for motif enrichment)
library(bedr)
# bed_candidates<-Annotate %>% transmute(chr=chr, start=pos-20, end=pos+20, Name)
# bed <- bed_candidates[,c('chr', 'start', 'end', 'Name')]
# Test<-get.fasta(bed, fasta = "../2_Output/GRCh37.primary_assembly.genome.fa")
write.table(bed_mr.heart, "../3_Results/Motif_Analysis/bed_validated.heart.bed",quote=FALSE,
row.names=FALSE,col.names=FALSE,sep="\t")
#Blood
bed_blood<-Blood_Validated %>% dplyr::select(chr, pos, Methylation_iPSC) %>% transmute(seqnames=chr, start=pos-10, end=pos+10, width = 21, strand = "*", deltaMeth=Methylation_iPSC)
bed_mr.blood<-as(bed_blood, "GRanges")
#Export genes as a bed file (for motif enrichment)
library(bedr)
# bed_candidates<-Annotate %>% transmute(chr=chr, start=pos-20, end=pos+20, Name)
# bed <- bed_candidates[,c('chr', 'start', 'end', 'Name')]
# Test<-get.fasta(bed, fasta = "../2_Output/GRCh37.primary_assembly.genome.fa")
write.table(bed_mr.blood, "../3_Results/Motif_Analysis/bed_validated.blood.bed",quote=FALSE,
row.names=FALSE,col.names=FALSE,sep="\t")CREB1 Targets
Within the CpG most strongly associated with DCM-obtained serum iPSC treatmap (, ATG7 promoter), the CREB1 binding site was identified as an overlapping motif. To identify other differentially-methylated CpG sites which also possess a CREB1 motif, PWMScan was used to identify all putative response elements. This list of genomic coordinates was then annotated using HOMER (Hg19) to determine relative proximity to known genes.
Need to intersect the bed file with the DMP list (iPSCs): Run the following in command-line: bedtools intersect -a \[CREB1 target bed file\] -b \[DMPs bed file\] > CREB1_DMPs.txt annotatePeaks.pl CREB1_DMPs.txt hg19 -annStats annotation_stats.txt > CREB1_DMPs.Annotated.txt
library(openxlsx)
#Import PWMScan CREB1 genomic motifs
CREB1_DMPs<-read.xlsx("../3_Results/CREB1_Targets/CREB1_DMPs.Annotated.xlsx") %>% filter(grepl("TSS", Annotation))
rownames(CREB1_DMPs)<-CREB1_DMPs$`PeakID.(cmd=annotatePeaks.pl.CREB1_DMPs.txt.hg19.-annStats.Test.txt)`
iPSC_DMPs<-read.xlsx("../2_Output/iPSC_DCM_vs_CON/iPSC_DCM_vs_CON_DMPs.xlsx", sheet = "P_0.05", rowNames = T)
CREB1_DMPs.All<-merge(CREB1_DMPs, iPSC_DMPs, by = 0)
write.xlsx(CREB1_DMPs.All, "CREB1_DMPs.xlsx")Supplemental Table: R Session Information
All packages and setting are acquired using the following command:
options(kableExtra.latex.load_packages = FALSE)
Run_tE<-Sys.time()
Run_time<-Run_tE - Run_tS
Run_time## Time difference of 10.86607 minslibrary(kableExtra)
sinfo<-devtools::session_info()
sinfo$platform## setting value
## version R version 4.1.2 (2021-11-01)
## os macOS Big Sur 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Berlin
## date 2022-01-17
## pandoc 2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)sinfo$packages %>% kable(
align="c",
caption="Packages and Required Dependencies") %>%
kable_styling(latex_options=c("repeat_header", "condensed"))| package | ondiskversion | loadedversion | path | loadedpath | attached | is_base | date | source | md5ok | library | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| abind | abind | 1.4.5 | 1.4-5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/abind | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/abind | FALSE | FALSE | 2016-07-21 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| annotate | annotate | 1.72.0 | 1.72.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/annotate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/annotate | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| AnnotationDbi | AnnotationDbi | 1.56.2 | 1.56.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/AnnotationDbi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/AnnotationDbi | TRUE | FALSE | 2021-11-09 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| askpass | askpass | 1.1 | 1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/askpass | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/askpass | FALSE | FALSE | 2019-01-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| assertthat | assertthat | 0.2.1 | 0.2.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/assertthat | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/assertthat | FALSE | FALSE | 2019-03-21 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| backports | backports | 1.4.1 | 1.4.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/backports | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/backports | FALSE | FALSE | 2021-12-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| base64 | base64 | 2.0 | 2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64 | FALSE | FALSE | 2016-05-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| base64enc | base64enc | 0.1.3 | 0.1-3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64enc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/base64enc | FALSE | FALSE | 2015-07-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| beanplot | beanplot | 1.2 | 1.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beanplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beanplot | FALSE | FALSE | 2014-09-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bedr | bedr | 1.0.7 | 1.0.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bedr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bedr | TRUE | FALSE | 2019-04-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Biobase | Biobase | 2.54.0 | 2.54.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biobase | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biobase | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocFileCache | BiocFileCache | 2.2.0 | 2.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocFileCache | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocFileCache | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocGenerics | BiocGenerics | 0.40.0 | 0.40.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocGenerics | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocGenerics | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocIO | BiocIO | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocIO | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocIO | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| BiocParallel | BiocParallel | 1.28.3 | 1.28.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocParallel | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BiocParallel | FALSE | FALSE | 2021-12-09 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| biomaRt | biomaRt | 2.50.1 | 2.50.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/biomaRt | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/biomaRt | TRUE | FALSE | 2021-11-21 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Biostrings | Biostrings | 2.62.0 | 2.62.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bit | bit | 4.0.4 | 4.0.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit | FALSE | FALSE | 2020-08-04 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bit64 | bit64 | 4.0.5 | 4.0.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit64 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bit64 | FALSE | FALSE | 2020-08-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bitops | bitops | 1.0.7 | 1.0-7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bitops | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bitops | FALSE | FALSE | 2021-04-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| blob | blob | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/blob | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/blob | FALSE | FALSE | 2021-07-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| broom | broom | 0.7.11 | 0.7.11 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/broom | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/broom | FALSE | FALSE | 2022-01-03 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bslib | bslib | 0.3.1 | 0.3.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bslib | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bslib | FALSE | FALSE | 2021-10-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| bumphunter | bumphunter | 1.36.0 | 1.36.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bumphunter | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bumphunter | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cachem | cachem | 1.0.6 | 1.0.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cachem | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cachem | FALSE | FALSE | 2021-08-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| calibrate | calibrate | 1.7.7 | 1.7.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/calibrate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/calibrate | TRUE | FALSE | 2020-06-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| callr | callr | 3.7.0 | 3.7.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/callr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/callr | FALSE | FALSE | 2021-04-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| car | car | 3.0.12 | 3.0-12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/car | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/car | FALSE | FALSE | 2021-11-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| carData | carData | 3.0.5 | 3.0-5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/carData | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/carData | FALSE | FALSE | 2022-01-06 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cellranger | cellranger | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cellranger | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cellranger | FALSE | FALSE | 2016-07-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| checkmate | checkmate | 2.0.0 | 2.0.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/checkmate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/checkmate | FALSE | FALSE | 2020-02-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| circlize | circlize | 0.4.13 | 0.4.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/circlize | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/circlize | TRUE | FALSE | 2021-06-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cli | cli | 3.1.0 | 3.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cli | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cli | FALSE | FALSE | 2021-10-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| clue | clue | 0.3.60 | 0.3-60 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/clue | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/clue | FALSE | FALSE | 2021-10-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cluster | cluster | 2.1.2 | 2.1.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cluster | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cluster | FALSE | FALSE | 2021-04-17 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| CMplot | CMplot | 3.7.0 | 3.7.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CMplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CMplot | TRUE | FALSE | 2021-10-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| codetools | codetools | 0.2.18 | 0.2-18 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/codetools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/codetools | FALSE | FALSE | 2020-11-04 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| colorspace | colorspace | 2.0.2 | 2.0-2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/colorspace | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/colorspace | FALSE | FALSE | 2021-06-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ComplexHeatmap | ComplexHeatmap | 2.11.1 | 2.11.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ComplexHeatmap | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ComplexHeatmap | TRUE | FALSE | 2021-11-26 | Github (jokergoo/ComplexHeatmap@826b321e721a9b1d683d060010cf6275618ae125) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| corrplot | corrplot | 0.92 | 0.92 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/corrplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/corrplot | TRUE | FALSE | 2021-11-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| cowplot | cowplot | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cowplot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cowplot | TRUE | FALSE | 2020-12-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| crayon | crayon | 1.4.2 | 1.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crayon | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crayon | FALSE | FALSE | 2021-10-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| crosstalk | crosstalk | 1.2.0 | 1.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crosstalk | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/crosstalk | FALSE | FALSE | 2021-11-04 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| curl | curl | 4.3.2 | 4.3.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/curl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/curl | FALSE | FALSE | 2021-06-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| data.table | data.table | 1.14.2 | 1.14.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/data.table | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/data.table | TRUE | FALSE | 2021-09-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DBI | DBI | 1.1.2 | 1.1.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DBI | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DBI | FALSE | FALSE | 2021-12-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| dbplyr | dbplyr | 2.1.1 | 2.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dbplyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dbplyr | FALSE | FALSE | 2021-04-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DelayedArray | DelayedArray | 0.20.0 | 0.20.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedArray | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedArray | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DelayedMatrixStats | DelayedMatrixStats | 1.16.0 | 1.16.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedMatrixStats | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DelayedMatrixStats | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| desc | desc | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/desc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/desc | FALSE | FALSE | 2021-09-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| DESeq2 | DESeq2 | 1.34.0 | 1.34.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DESeq2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/DESeq2 | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| devtools | devtools | 2.4.3 | 2.4.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/devtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/devtools | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| digest | digest | 0.6.29 | 0.6.29 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest | FALSE | FALSE | 2021-12-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| doParallel | doParallel | 1.0.16 | 1.0.16 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doParallel | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doParallel | FALSE | FALSE | 2020-10-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| doRNG | doRNG | 1.8.2 | 1.8.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doRNG | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/doRNG | FALSE | FALSE | 2020-01-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| dplyr | dplyr | 1.0.7 | 1.0.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dplyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/dplyr | TRUE | FALSE | 2021-06-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ellipsis | ellipsis | 0.3.2 | 0.3.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ellipsis | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ellipsis | FALSE | FALSE | 2021-04-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| evaluate | evaluate | 0.14 | 0.14 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/evaluate | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/evaluate | FALSE | FALSE | 2019-05-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| fansi | fansi | 1.0.0 | 1.0.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fansi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fansi | FALSE | FALSE | 2022-01-10 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| farver | farver | 2.1.0 | 2.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/farver | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/farver | FALSE | FALSE | 2021-02-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| fastmap | fastmap | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fastmap | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fastmap | FALSE | FALSE | 2021-01-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ff | ff | 4.0.5 | 4.0.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ff | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ff | FALSE | FALSE | 2021-10-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| filelock | filelock | 1.0.2 | 1.0.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/filelock | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/filelock | FALSE | FALSE | 2018-10-05 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| foreach | foreach | 1.5.1 | 1.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreach | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreach | TRUE | FALSE | 2020-10-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| foreign | foreign | 0.8.81 | 0.8-81 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreign | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/foreign | FALSE | FALSE | 2020-12-22 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| formatR | formatR | 1.11 | 1.11 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/formatR | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/formatR | FALSE | FALSE | 2021-06-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Formula | Formula | 1.2.4 | 1.2-4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Formula | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Formula | TRUE | FALSE | 2020-10-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| fs | fs | 1.5.2 | 1.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fs | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/fs | FALSE | FALSE | 2021-12-08 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| futile.logger | futile.logger | 1.4.3 | 1.4.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.logger | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.logger | TRUE | FALSE | 2016-07-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| futile.options | futile.options | 1.0.1 | 1.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.options | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/futile.options | FALSE | FALSE | 2018-04-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| genefilter | genefilter | 1.76.0 | 1.76.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/genefilter | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/genefilter | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| geneplotter | geneplotter | 1.72.0 | 1.72.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/geneplotter | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/geneplotter | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| generics | generics | 0.1.1 | 0.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/generics | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/generics | FALSE | FALSE | 2021-10-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomeInfoDb | GenomeInfoDb | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDb | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDb | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomeInfoDbData | GenomeInfoDbData | 1.2.7 | 1.2.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDbData | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomeInfoDbData | FALSE | FALSE | 2021-11-17 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomicAlignments | GenomicAlignments | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicAlignments | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicAlignments | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomicFeatures | GenomicFeatures | 1.46.3 | 1.46.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicFeatures | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicFeatures | TRUE | FALSE | 2021-12-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GenomicRanges | GenomicRanges | 1.46.1 | 1.46.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicRanges | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GenomicRanges | TRUE | FALSE | 2021-11-18 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GEOquery | GEOquery | 2.62.2 | 2.62.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GEOquery | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GEOquery | FALSE | FALSE | 2022-01-11 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GetoptLong | GetoptLong | 1.0.5 | 1.0.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GetoptLong | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GetoptLong | FALSE | FALSE | 2020-12-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggplot2 | ggplot2 | 3.3.5 | 3.3.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggplot2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggplot2 | TRUE | FALSE | 2021-06-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggpubr | ggpubr | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggpubr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggpubr | TRUE | FALSE | 2020-06-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggrepel | ggrepel | 0.9.1 | 0.9.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggrepel | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggrepel | TRUE | FALSE | 2021-01-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ggsignif | ggsignif | 0.6.3 | 0.6.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggsignif | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggsignif | TRUE | FALSE | 2021-09-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| GlobalOptions | GlobalOptions | 0.1.2 | 0.1.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GlobalOptions | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/GlobalOptions | FALSE | FALSE | 2020-06-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| glue | glue | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/glue | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/glue | FALSE | FALSE | 2021-12-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| gridExtra | gridExtra | 2.3 | 2.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gridExtra | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gridExtra | TRUE | FALSE | 2017-09-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| gtable | gtable | 0.3.0 | 0.3.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtable | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtable | FALSE | FALSE | 2019-03-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| gtools | gtools | 3.9.2 | 3.9.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/gtools | TRUE | FALSE | 2021-06-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Haplin | Haplin | 7.2.3 | 7.2.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Haplin | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Haplin | TRUE | FALSE | 2020-09-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| HDF5Array | HDF5Array | 1.22.1 | 1.22.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/HDF5Array | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/HDF5Array | FALSE | FALSE | 2021-11-14 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| highr | highr | 0.9 | 0.9 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/highr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/highr | FALSE | FALSE | 2021-04-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Hmisc | Hmisc | 4.6.0 | 4.6-0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Hmisc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Hmisc | TRUE | FALSE | 2021-10-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| hms | hms | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/hms | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/hms | FALSE | FALSE | 2021-09-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| htmlTable | htmlTable | 2.4.0 | 2.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlTable | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlTable | FALSE | FALSE | 2022-01-04 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| htmltools | htmltools | 0.5.2 | 0.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmltools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmltools | FALSE | FALSE | 2021-08-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| htmlwidgets | htmlwidgets | 1.5.4 | 1.5.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlwidgets | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlwidgets | FALSE | FALSE | 2021-09-08 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| httpuv | httpuv | 1.6.5 | 1.6.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httpuv | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httpuv | FALSE | FALSE | 2022-01-05 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| httr | httr | 1.4.2 | 1.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/httr | FALSE | FALSE | 2020-07-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| IlluminaHumanMethylation450kanno.ilmn12.hg19 | IlluminaHumanMethylation450kanno.ilmn12.hg19 | 0.6.0 | 0.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kanno.ilmn12.hg19 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kanno.ilmn12.hg19 | TRUE | FALSE | 2021-11-17 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| IlluminaHumanMethylation450kmanifest | IlluminaHumanMethylation450kmanifest | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kmanifest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IlluminaHumanMethylation450kmanifest | TRUE | FALSE | 2021-11-17 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| illuminaio | illuminaio | 0.36.0 | 0.36.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/illuminaio | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/illuminaio | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| IRanges | IRanges | 2.28.0 | 2.28.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| iterators | iterators | 1.0.13 | 1.0.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/iterators | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/iterators | TRUE | FALSE | 2020-10-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| jpeg | jpeg | 0.1.9 | 0.1-9 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jpeg | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jpeg | FALSE | FALSE | 2021-07-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| jquerylib | jquerylib | 0.1.4 | 0.1.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jquerylib | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jquerylib | FALSE | FALSE | 2021-04-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| jsonlite | jsonlite | 1.7.2 | 1.7.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jsonlite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/jsonlite | FALSE | FALSE | 2020-12-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| kableExtra | kableExtra | 1.3.4 | 1.3.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/kableExtra | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/kableExtra | TRUE | FALSE | 2021-02-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| KEGGREST | KEGGREST | 1.34.0 | 1.34.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/KEGGREST | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/KEGGREST | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| knitr | knitr | 1.37 | 1.37 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/knitr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/knitr | TRUE | FALSE | 2021-12-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| labeling | labeling | 0.4.2 | 0.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/labeling | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/labeling | FALSE | FALSE | 2020-10-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lambda.r | lambda.r | 1.2.4 | 1.2.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lambda.r | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lambda.r | FALSE | FALSE | 2019-09-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| later | later | 1.3.0 | 1.3.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/later | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/later | FALSE | FALSE | 2021-08-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lattice | lattice | 0.20.45 | 0.20-45 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lattice | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lattice | TRUE | FALSE | 2021-09-22 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| latticeExtra | latticeExtra | 0.6.29 | 0.6-29 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/latticeExtra | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/latticeExtra | FALSE | FALSE | 2019-12-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lazyeval | lazyeval | 0.2.2 | 0.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lazyeval | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lazyeval | FALSE | FALSE | 2019-03-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| lifecycle | lifecycle | 1.0.1 | 1.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lifecycle | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/lifecycle | FALSE | FALSE | 2021-09-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| limma | limma | 3.50.0 | 3.50.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/limma | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/limma | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| locfit | locfit | 1.5.9.4 | 1.5-9.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/locfit | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/locfit | TRUE | FALSE | 2020-03-25 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| magick | magick | 2.7.3 | 2.7.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magick | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magick | FALSE | FALSE | 2021-08-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| magrittr | magrittr | 2.0.1 | 2.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magrittr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/magrittr | TRUE | FALSE | 2020-11-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| MASS | MASS | 7.3.54 | 7.3-54 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS | TRUE | FALSE | 2021-05-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Matrix | Matrix | 1.4.0 | 1.4-0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix | FALSE | FALSE | 2021-12-08 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| MatrixGenerics | MatrixGenerics | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MatrixGenerics | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/MatrixGenerics | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| matrixStats | matrixStats | 0.61.0 | 0.61.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/matrixStats | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/matrixStats | TRUE | FALSE | 2021-09-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| mclust | mclust | 5.4.9 | 5.4.9 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mclust | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mclust | FALSE | FALSE | 2021-12-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| memoise | memoise | 2.0.1 | 2.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/memoise | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/memoise | FALSE | FALSE | 2021-11-26 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| mgcv | mgcv | 1.8.38 | 1.8-38 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mgcv | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mgcv | FALSE | FALSE | 2021-10-06 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| mime | mime | 0.12 | 0.12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mime | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/mime | FALSE | FALSE | 2021-09-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| minfi | minfi | 1.40.0 | 1.40.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/minfi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/minfi | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| multtest | multtest | 2.50.0 | 2.50.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/multtest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/multtest | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| munsell | munsell | 0.5.0 | 0.5.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/munsell | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/munsell | FALSE | FALSE | 2018-06-12 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| nlme | nlme | 3.1.153 | 3.1-153 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nlme | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nlme | FALSE | FALSE | 2021-09-07 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| nnet | nnet | 7.3.16 | 7.3-16 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nnet | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nnet | FALSE | FALSE | 2021-05-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| nor1mix | nor1mix | 1.3.0 | 1.3-0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nor1mix | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/nor1mix | FALSE | FALSE | 2019-06-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| openssl | openssl | 1.4.6 | 1.4.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl | FALSE | FALSE | 2021-12-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| openxlsx | openxlsx | 4.2.5 | 4.2.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openxlsx | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/openxlsx | TRUE | FALSE | 2021-12-14 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pacman | pacman | 0.5.1 | 0.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pacman | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pacman | TRUE | FALSE | 2019-03-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pheatmap | pheatmap | 1.0.12 | 1.0.12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pheatmap | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pheatmap | TRUE | FALSE | 2019-01-04 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pillar | pillar | 1.6.4 | 1.6.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pillar | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pillar | FALSE | FALSE | 2021-10-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pkgbuild | pkgbuild | 1.3.1 | 1.3.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgbuild | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgbuild | FALSE | FALSE | 2021-12-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pkgconfig | pkgconfig | 2.0.3 | 2.0.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgconfig | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgconfig | FALSE | FALSE | 2019-09-22 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| pkgload | pkgload | 1.2.4 | 1.2.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgload | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pkgload | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| plotly | plotly | 4.10.0 | 4.10.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plotly | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plotly | TRUE | FALSE | 2021-10-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| plyr | plyr | 1.8.6 | 1.8.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/plyr | FALSE | FALSE | 2020-03-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| png | png | 0.1.7 | 0.1-7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/png | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/png | FALSE | FALSE | 2013-12-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| preprocessCore | preprocessCore | 1.56.0 | 1.56.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| prettyunits | prettyunits | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/prettyunits | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/prettyunits | FALSE | FALSE | 2020-01-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| processx | processx | 3.5.2 | 3.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/processx | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/processx | FALSE | FALSE | 2021-04-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| progress | progress | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/progress | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/progress | FALSE | FALSE | 2019-05-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| promises | promises | 1.2.0.1 | 1.2.0.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/promises | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/promises | FALSE | FALSE | 2021-02-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| ps | ps | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ps | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ps | FALSE | FALSE | 2021-02-28 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| purrr | purrr | 0.3.4 | 0.3.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/purrr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/purrr | FALSE | FALSE | 2020-04-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| quadprog | quadprog | 1.5.8 | 1.5-8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/quadprog | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/quadprog | FALSE | FALSE | 2019-11-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R.methodsS3 | R.methodsS3 | 1.8.1 | 1.8.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.methodsS3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.methodsS3 | FALSE | FALSE | 2020-08-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R.oo | R.oo | 1.24.0 | 1.24.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.oo | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.oo | FALSE | FALSE | 2020-08-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R.utils | R.utils | 2.11.0 | 2.11.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.utils | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R.utils | FALSE | FALSE | 2021-09-26 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| R6 | R6 | 2.5.1 | 2.5.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/R6 | FALSE | FALSE | 2021-08-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rappdirs | rappdirs | 0.3.3 | 0.3.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rappdirs | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rappdirs | FALSE | FALSE | 2021-01-31 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| RColorBrewer | RColorBrewer | 1.1.2 | 1.1-2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RColorBrewer | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RColorBrewer | TRUE | FALSE | 2014-12-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Rcpp | Rcpp | 1.0.7 | 1.0.7 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp | FALSE | FALSE | 2021-07-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| RCurl | RCurl | 1.98.1.5 | 1.98-1.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RCurl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RCurl | FALSE | FALSE | 2021-09-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| readr | readr | 2.1.1 | 2.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readr | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| readxl | readxl | 1.3.1 | 1.3.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readxl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/readxl | TRUE | FALSE | 2019-03-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| remotes | remotes | 2.4.2 | 2.4.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/remotes | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/remotes | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| reshape | reshape | 0.8.8 | 0.8.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape | FALSE | FALSE | 2018-10-23 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| reshape2 | reshape2 | 1.4.4 | 1.4.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/reshape2 | TRUE | FALSE | 2020-04-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| restfulr | restfulr | 0.0.13 | 0.0.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/restfulr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/restfulr | FALSE | FALSE | 2017-08-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rhdf5 | rhdf5 | 2.38.0 | 2.38.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5 | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rhdf5filters | rhdf5filters | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5filters | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rhdf5filters | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Rhdf5lib | Rhdf5lib | 1.16.0 | 1.16.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rjson | rjson | 0.2.21 | 0.2.21 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rjson | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rjson | FALSE | FALSE | 2022-01-09 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rlang | rlang | 0.4.12 | 0.4.12 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rlang | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rlang | FALSE | FALSE | 2021-10-18 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rmarkdown | rmarkdown | 2.11 | 2.11 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown | FALSE | FALSE | 2021-09-14 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rngtools | rngtools | 1.5.2 | 1.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rngtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rngtools | FALSE | FALSE | 2021-09-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rpart | rpart | 4.1.15 | 4.1-15 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rpart | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rpart | FALSE | FALSE | 2019-04-12 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rprojroot | rprojroot | 2.0.2 | 2.0.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rprojroot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rprojroot | FALSE | FALSE | 2020-11-15 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| Rsamtools | Rsamtools | 2.10.0 | 2.10.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rsamtools | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rsamtools | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| RSQLite | RSQLite | 2.2.9 | 2.2.9 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RSQLite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RSQLite | FALSE | FALSE | 2021-12-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rstatix | rstatix | 0.7.0 | 0.7.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstatix | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstatix | FALSE | FALSE | 2021-02-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rstudioapi | rstudioapi | 0.13 | 0.13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstudioapi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rstudioapi | FALSE | FALSE | 2020-11-12 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rtracklayer | rtracklayer | 1.54.0 | 1.54.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rtracklayer | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rtracklayer | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| rvest | rvest | 1.0.2 | 1.0.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rvest | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rvest | FALSE | FALSE | 2021-10-16 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| S4Vectors | S4Vectors | 0.32.3 | 0.32.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors | TRUE | FALSE | 2021-11-21 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| sass | sass | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sass | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sass | FALSE | FALSE | 2021-05-12 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| scales | scales | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scales | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scales | FALSE | FALSE | 2020-05-11 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| scrime | scrime | 1.3.5 | 1.3.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scrime | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/scrime | FALSE | FALSE | 2018-12-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| sessioninfo | sessioninfo | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sessioninfo | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sessioninfo | FALSE | FALSE | 2021-12-06 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| shape | shape | 1.4.6 | 1.4.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shape | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shape | FALSE | FALSE | 2021-05-19 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| shiny | shiny | 1.7.1 | 1.7.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shiny | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shiny | TRUE | FALSE | 2021-10-02 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| shinyMethyl | shinyMethyl | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shinyMethyl | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/shinyMethyl | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| siggenes | siggenes | 1.68.0 | 1.68.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/siggenes | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/siggenes | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| sparseMatrixStats | sparseMatrixStats | 1.6.0 | 1.6.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sparseMatrixStats | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sparseMatrixStats | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| stringi | stringi | 1.7.6 | 1.7.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringi | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringi | FALSE | FALSE | 2021-11-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| stringr | stringr | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/stringr | TRUE | FALSE | 2019-02-10 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| SummarizedExperiment | SummarizedExperiment | 1.24.0 | 1.24.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/SummarizedExperiment | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/SummarizedExperiment | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| survival | survival | 3.2.13 | 3.2-13 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/survival | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/survival | TRUE | FALSE | 2021-08-24 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| svglite | svglite | 2.0.0 | 2.0.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/svglite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/svglite | FALSE | FALSE | 2021-02-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| systemfonts | systemfonts | 1.0.3 | 1.0.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/systemfonts | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/systemfonts | FALSE | FALSE | 2021-10-13 | CRAN (R 4.1.2) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| testthat | testthat | 3.1.1 | 3.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat | FALSE | FALSE | 2021-12-03 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tibble | tibble | 3.1.6 | 3.1.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tibble | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tibble | FALSE | FALSE | 2021-11-07 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tidyr | tidyr | 1.1.4 | 1.1.4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyr | TRUE | FALSE | 2021-09-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tidyselect | tidyselect | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyselect | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tidyselect | FALSE | FALSE | 2021-04-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| tzdb | tzdb | 0.2.0 | 0.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tzdb | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/tzdb | FALSE | FALSE | 2021-10-27 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| usethis | usethis | 2.1.5 | 2.1.5 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/usethis | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/usethis | FALSE | FALSE | 2021-12-09 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| utf8 | utf8 | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/utf8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/utf8 | FALSE | FALSE | 2021-07-24 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| vctrs | vctrs | 0.3.8 | 0.3.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/vctrs | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/vctrs | FALSE | FALSE | 2021-04-29 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| VennDiagram | VennDiagram | 1.7.1 | 1.7.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/VennDiagram | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/VennDiagram | TRUE | FALSE | 2021-12-02 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| viridisLite | viridisLite | 0.4.0 | 0.4.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/viridisLite | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/viridisLite | FALSE | FALSE | 2021-04-13 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| webshot | webshot | 0.5.2 | 0.5.2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/webshot | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/webshot | FALSE | FALSE | 2019-11-22 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| wesanderson | wesanderson | 0.3.6 | 0.3.6 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/wesanderson | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/wesanderson | TRUE | FALSE | 2018-04-20 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| withr | withr | 2.4.3 | 2.4.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/withr | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/withr | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| xfun | xfun | 0.29 | 0.29 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xfun | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xfun | FALSE | FALSE | 2021-12-14 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| XML | XML | 3.99.0.8 | 3.99-0.8 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XML | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XML | FALSE | FALSE | 2021-09-17 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| xml2 | xml2 | 1.3.3 | 1.3.3 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xml2 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xml2 | FALSE | FALSE | 2021-11-30 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| xtable | xtable | 1.8.4 | 1.8-4 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xtable | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/xtable | FALSE | FALSE | 2019-04-21 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| XVector | XVector | 0.34.0 | 0.34.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector | TRUE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| yaml | yaml | 2.2.1 | 2.2.1 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/yaml | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/yaml | FALSE | FALSE | 2020-02-01 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| zip | zip | 2.2.0 | 2.2.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zip | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zip | FALSE | FALSE | 2021-05-31 | CRAN (R 4.1.0) | /Library/Frameworks/R.framework/Versions/4.1/Resources/library | |
| zlibbioc | zlibbioc | 1.40.0 | 1.40.0 | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc | /Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc | FALSE | FALSE | 2021-10-26 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.1/Resources/library |